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Papers of Note: Jan 18, 2011


Rapid detection of genetic variants in hypertrophic cardiomyopathy by custom DNA resequencing array in clinical practice.
Fokstuen S, Munoz A, Melacini P, Iliceto S, et al.
J Med Genet. 2011 Jan 14. [Epub ahead of print]

A comprehensive study of multiple mapping and feature selection for correction strategy in the analysis of small RNAs from SOLiD sequencing.
Guo L, Liang T, Lu Z.
Biosystems. 2011 Jan 12. [Epub ahead of print]

Systematic cross-validation of 454 sequencing and pyrosequencing for the exact quantification of DNA methylation patterns with single CpG resolution.
Potapova A, Albat C, Hasemeier B, Hauszler K, et al.
BMC Biotechnol. 2011 Jan 14;11(1):6. [Epub ahead of print]

Resequencing of 29 candidate genes in patients with familial and sporadic amyotrophic lateral sclerosis.
Daoud H, Valdmanis PN, Gros-Louis F, Belzil V, et al.
Arch Neurol. 2011 Jan 10. [Epub ahead of print]

Transpositional landscape of rice genome revealed by paired-end mapping of high-throughput resequencing data.
Sabot F, Picault N, Elbaidouri M, Llauro C, et al.
Plant J. 2011 Jan 10. doi: 10.1111/j.1365-313X.2011.04492.x. [Epub ahead of print]

Robust computational analysis of rRNA hypervariable tag datasets.
Sipos M, Jeraldo P, Chia N, Qu A, et al.
PLoS One. 2010 Dec 31;5(12):e15220.

De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification.
Garg R, Patel RK, Tyagi AK, Jain M.
DNA Res. 2011 Jan 7. [Epub ahead of print]

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers.
Marçais G, Kingsford C.
Bioinformatics. 2011 Jan 7. [Epub ahead of print]

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X-MATE: A flexible system for mapping short read data.
Wood DL, Xu Q, Pearson JV, Cloonan N, Grimmond SM.
Bioinformatics. 2011 Jan 6. [Epub ahead of print]

Detecting structural variations in the human genome using next generation sequencing.
Xi R, Kim TM, Park PJ.
Brief Funct Genomics. 2011 Jan 6. [Epub ahead of print]

Massive genomic rearrangement acquired in a single catastrophic event during cancer development.
Stephens PJ, Greenman CD, Fu B, Yang F, et al.
Cell. 2011 Jan 7;144(1):27-40.

The complete genomic sequence of HLA-DRB1*10:01:01 was identified by sequencing in a Han Chinese individual.
Liu B, Xiong Y, Tian C, Zhong Y, Liu SM.
Tissue Antigens. 2011 Feb;77(2):159-60. doi: 10.1111/j.1399-0039.2010.01593.x.

Quantification of gene transcripts with deep sequencing analysis of gene expression (DSAGE) using 1 to 2 µg total RNA.
C Christodoulou D, Gorham JM, Kawana M, Depalma SR, et al.
Curr Protoc Mol Biol. 2011 Jan;Chapter 25:Unit25B.9.

Non-invasive prenatal assessment of trisomy 21 by multiplexed maternal plasma DNA sequencing: large scale validity study.
Chiu RW, Akolekar R, Zheng YW, Leung TY, et al.
BMJ. 2011 Jan 11;342:c7401. doi: 10.1136/bmj.c7401.

Evaluation of microsatellite variation in the 1000 Genomes Project pilot studies is indicative of the quality and utility of the raw data and alignments.
McIver LJ, Fondon JW 3rd, Skinner MA, Garner HR.
Genomics. 2011 Jan 8. [Epub ahead of print]

Controlled translocation of individual DNA molecules through protein nanopores with engineered molecular brakes.
Rincon-Restrepo M, Mikhailova E, Bayley H, Maglia G.
Nano Lett. 2011 Jan 11. [Epub ahead of print]

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Carrier testing for severe childhood recessive diseases by next-generation sequencing.
Bell CJ, Dinwiddie DL, Miller NA, Hateley SL, et al.
Sci Transl Med. 2011 Jan 12;3(65):65ra4.

Improved nucleotide selectivity and termination of 3'-OH unblocked reversible terminators by molecular tuning of 2-nitrobenzyl alkylated HOMedU triphosphates.
Litosh VA, Wu W, Stupi BP, Wang J, et al.
Nucleic Acids Res. 2011 Jan 11. [Epub ahead of print]

Shape-based peak identification for ChIP-seq.
Hower V, Evans SN, Pachter L.
BMC Bioinformatics. 2011 Jan 12;12(1):15.

Multiplexed shotgun genotyping for rapid and efficient genetic mapping.
Andolfatto P, Davison D, Erezyilmaz D, Hu TT, et al.
Genome Res. 2011 Jan 13. [Epub ahead of print]

Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering.
Hao X, Jiang R, Chen T.
Bioinformatics. 2011 Jan 13. [Epub ahead of print]

A pipeline for RNA-seq data processing and quality assessment.
Goncalves A, Tikhonov A, Brazma A, Kapushesky M.
Bioinformatics. 2011 Jan 13. [Epub ahead of print]

SAMMate: a GUI tool for processing short read alignments in SAM/BAM format.
Xu G, Deng N, Zhao Z, Judeh T, et al.
Source Code Biol Med. 2011 Jan 13;6(1):2. [Epub ahead of print]

Combining gene prediction methods to improve metagenomic gene annotation.
Yok NG, Rosen GL.
BMC Bioinformatics. 2011 Jan 13;12(1):20.

The Scan

US Booster Eligibility Decision

The US CDC director recommends that people at high risk of developing COVID-19 due to their jobs also be eligible for COVID-19 boosters, in addition to those 65 years old and older or with underlying medical conditions.

Arizona Bill Before Judge

The Arizona Daily Star reports that a judge is weighing whether a new Arizona law restricting abortion due to genetic conditions is a ban or a restriction.

Additional Genes

Wales is rolling out new genetic testing service for cancer patients, according to BBC News.

Science Papers Examine State of Human Genomic Research, Single-Cell Protein Quantification

In Science this week: a number of editorials and policy reports discuss advances in human genomic research, and more.